+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5gje | |||||||||
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タイトル | Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 | |||||||||
要素 |
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キーワード | SIGNALING PROTEIN / Wnt signaling / Wnt co-receptor / LRP6 / glycoprotein / antagonist / Dkk1 / conformational change | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation ...negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation / Wnt-Frizzled-LRP5/6 complex / motor learning / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / endoderm formation / synapse pruning / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / endocardial cushion development / regulation of receptor internalization / heart induction / receptor antagonist activity / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / co-receptor binding / Wnt receptor activity / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / Wnt-protein binding / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / heart valve development / frizzled binding / negative regulation of ossification / Wnt signalosome / neural crest cell differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / embryonic limb morphogenesis / face morphogenesis / limb development / low-density lipoprotein particle receptor binding / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / negative regulation of peptidyl-serine phosphorylation / negative regulation of smooth muscle cell apoptotic process / mesoderm formation / negative regulation of BMP signaling pathway / hair follicle development / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / regulation of neuron apoptotic process / response to retinoic acid / forebrain development / regulation of synaptic transmission, glutamatergic / Regulation of FZD by ubiquitination / negative regulation of protein binding / TCF dependent signaling in response to WNT / protein localization to plasma membrane / positive regulation of JNK cascade / growth factor activity / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / negative regulation of neuron projection development / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / learning or memory / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 21 Å | |||||||||
データ登録者 | Matoba, K. / Mihara, E. / Tamura-Kawakami, K. / Hirai, H. / Thompson, S. / Iwasaki, K. / Takagi, J. | |||||||||
引用 | ジャーナル: Cell Rep / 年: 2017 タイトル: Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1. 著者: Kyoko Matoba / Emiko Mihara / Keiko Tamura-Kawakami / Naoyuki Miyazaki / Shintaro Maeda / Hidenori Hirai / Samuel Thompson / Kenji Iwasaki / Junichi Takagi / 要旨: LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. ...LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. Although multiple crystal structures are available for fragments of the LRP6 ectodomain, we lack a consensus view on the overall molecular architecture of the full-length LRP6 and its dynamic aspects. Here, we used negative-stain electron microscopy to probe conformational states of the entire ectodomain of LRP6 in solution and found that the four-module ectodomain undergoes a large bending motion hinged at the junction between the second and the third modules. Importantly, the extent of inter-domain motion is modulated by evolutionarily conserved N-glycan chains proximal to the joint. We also found that the LRP6 ectodomain becomes highly compact upon complexation with the Wnt antagonist Dkk1, suggesting a potential role for the ectodomain conformational change in the regulation of receptor oligomerization and signaling. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5gje.cif.gz | 403.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5gje.ent.gz | 329.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5gje.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 5gje_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5gje_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 5gje_validation.xml.gz | 42.8 KB | 表示 | |
CIF形式データ | 5gje_validation.cif.gz | 64.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/gj/5gje ftp://data.pdbj.org/pub/pdb/validation_reports/gj/5gje | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-Low-density lipoprotein receptor-related protein ... , 2種, 2分子 AB
#1: タンパク質 | 分子量: 69034.883 Da / 分子数: 1 / 断片: UNP residues 20-630 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRP6 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: O75581 |
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#2: タンパク質 | 分子量: 69810.609 Da / 分子数: 1 / 断片: UNP residues 631-1246 / Mutation: V1062I / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRP6 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: O75581 |
-タンパク質 , 1種, 1分子 C
#3: タンパク質 | 分子量: 9607.076 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DKK1, UNQ492/PRO1008 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: O94907 |
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-糖 , 3種, 8分子
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #7: 糖 | |
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-非ポリマー , 3種, 16分子
#6: 化合物 | #8: 化合物 | ChemComp-GOL / | #9: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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分子量 | 値: 0.21 MDa / 実験値: NO | ||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.2 | ||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO / 詳細: This sample was monodisperse. | ||||||||||||||||||||||||||||
染色 | タイプ: NONE / 染色剤: Uranyl acetate | ||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. |
-電子顕微鏡撮影
顕微鏡 | モデル: HITACHI H-9500SD |
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電子銃 | 電子線源: LAB6 / 加速電圧: 200 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 80000 X / Cs: 2.8 mm |
試料ホルダ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
撮影 | 平均露光時間: 2 sec. / 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: TVIPS TEMCAM-F224 (2k x 2k) |
画像スキャン | サンプリングサイズ: 24 µm / 横: 2048 / 縦: 2048 |
-解析
EMソフトウェア |
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画像処理 | 詳細: The selected images were band-pass filtered. | ||||||||||||||||||||||||||||||||||||
CTF補正 | 詳細: This was not done for RCT but for following single-particle reconstruction タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
粒子像の選択 | 詳細: 10974 tilt pairs for RCT | ||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 21 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 5390 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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